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A Study of the Differential Expression Profiles of Keshan Disease Lncrna/Mrna Genes Based on RNA-Seq

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421 Original Article A study of the differential expression profiles of Keshan disease lncRNA/mRNA genes based on RNA-seq Guangyong Huang1, Jingwen Liu2, Yuehai Wang1, Youzhang Xiang3 1Department of Cardiology, Liaocheng People’s Hospital of Shandong University, Liaocheng, China; 2School of Nursing, Liaocheng Vocational & Technical College, Liaocheng, China; 3Shandong Institute for Endemic Disease Control, Jinan, China Contributions: (I) Conception and design: G Huang, Y Xiang; (II) Administrative support: G Huang, Y Wang; (III) Provision of study materials or patients: G Huang, J Liu, Y Xiang; (IV) Collection and assembly of data: G Huang, J Liu; (V) Data analysis and interpretation: J Liu, Y Wang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. Correspondence to: Guangyong Huang, MD, PhD. Department of Cardiology, Liaocheng People’s Hospital of Shandong University, No. 67 of Dongchang Street, Liaocheng 252000, China. Email: [email protected]. Background: This study aims to analyze the differential expression profiles of lncRNA in Keshan disease (KSD) and to explore the molecular mechanism of the disease occurrence and development. Methods: RNA-seq technology was used to construct the lncRNA/mRNA expression library of a KSD group (n=10) and a control group (n=10), and then Cuffdiff software was used to obtain the gene lncRNA/ mRNA FPKM value as the expression profile of lncRNA/mRNA. The fold changes between the two sets of samples were calculated to obtain differential lncRNA/mRNA expression profiles, and a bioinformatics analysis of differentially expressed genes was performed. Results: A total of 89,905 lncRNAs and 20,315 mRNAs were detected. Statistical analysis revealed that 921 lncRNAs had obvious differential expression, among which 36 were up-regulated and 885 were down- regulated; 2,771 mRNAs presented with obvious differential expression, among which 253 were up-regulated and 2,518 were down-regulated, and cluster analysis indicated that the gene expression trends among the sample groups were consistent. The differentially expressed lncRNAs were tested for target genes, and 117 genes were found to be regulated by differential lncRNAs, which were concentrated in six signaling pathways, among which the apoptosis FoxO signaling pathway ranked first, so the target genes IGF1R and TGFB2 were screened out. Conclusions: In this study, RNA-seq technology was used to obtain the differential gene expression profiles of KSD, and bioinformatics analysis was performed to screen out target genes, pointing out the direction for further research into the etiology, pathogenesis and drug treatment targets of KSD. Keywords: Keshan disease (KSD); long noncoding RNA; messenger RNA; RNA sequencing Submitted Aug 27, 2020. Accepted for publication Nov 29, 2020. doi: 10.21037/cdt-20-746 View this article at: http://dx.doi.org/10.21037/cdt-20-746 Introduction manifestations are ventricular enlargement and a decrease in myocardial contractility, which often causes heart failure, Keshan disease (KSD) is an endemic cardiomyopathy unique arrhythmia and even sudden death. Thus, the prognosis is poor. to China, and patients are mainly found in the narrow and The cause of KSD is not yet fully understood, but low-selenium zone from the northeast to the southwest of research results confirm there exists a close association China. According to statistics (1), 16 provinces (regions), between low selenium levels and KSD (2,3). As an essential with a population of 60 million, are affected. KSD is mainly trace element, selenium realizes its biological function characterized by myocardial involvement, and the clinical mainly through selenoproteins. At present, a large number © Cardiovascular Diagnosis and Therapy. All rights reserved. Cardiovasc Diagn Ther 2021;11(2):411-421 | http://dx.doi.org/10.21037/cdt-20-746 412 name Table 1 Clinical data of the KSD group and control group NYHA Number Gender Systolic blood Diastolic blood Heart rate Group Age (Y) LA (mm) LV (mm) LVEF (%) classification of cases (M/F) pressure (mmHg) pressure (mmHg) (times/min) (I/II/III/IV) KSD group 10 4/6 50.9±7.3 116.6±16.0 74.6±10.0 73.9±11.3 40.6±3.0* 59.7±2.9* 35.6±4.6* 0/7/3/0* Control group 10 5/5 45.5±4.9 121.0±5.2 75.8±4.2 68.1±4.4 32.0±1.9 45.6±2.2 67.8±3.2 10/0/0/0 t or χ2 0.20 1.94 0.83 0.35 1.51 7.66 12.25 18.17 40.0 Compared with control group, *, P<0.01. LA, left atrial diameter; LV, left ventricular end-diastolic diameter; LVEF, left ventricular ejection fraction; NYHA, American College of Cardiology; KSD, Keshan disease. of studies have revealed that selenium deficiency is closely analyzed by means of bioinformatics, providing a theoretical related to the occurrence and development of KSD. The basis for shedding light on the mechanism of disease at the selenium content of the environment of the KSD area, level of gene expression regulation. as found in the soil, local food, and hair and blood of the We present the following article in accordance with people, and the plasma selenoprotein P are lower than those the MDAR reporting checklist (available at: http://dx.doi. in non-affected areas (4,5). A systematic review and meta- org/10.21037/cdt-20-746). analysis of selenium deficiency and KSD revealed that the supplementation of selenium could significantly reduce the Methods incidence of KSD (2). Current studies suggest that the mechanism of chronic Clinical data KSD is mainly related to mitochondrial oxidative damage, Ten KSD patients in the severe KSD area of Shandong apoptosis and fibrosis regulation (6-8). Low selenium can Province were enrolled as the KSD group. There were five cause damage to myocardial mitochondria, and selenium male patients and five female patients, ranging from 38 to deficiency can lead to a decrease in the synthesis of 45 years of age, with an average age of 42.6 years. All the glutathione peroxidase. This then leads to the aggravation patients had their medical histories taken, and underwent of oxidative stress damage, in turn causing myocardial a physical examination, electrocardiography, X-ray damage and, ultimately, resulting in cardiomyopathy. photography, cardiac ultrasound and related biochemical Selenium deficiency may also amplify other pathogenic examinations, and the examination results met the factors, including viral and other infections (3). Recent diagnostic criteria of KSD (GB17021-1997). In addition, comparative studies on the gene expression of KSD 10 healthy people, five males and five females, were and dilated cardiomyopathy have found that KSD and enrolled locally as the control group, having undergone a dilated cardiomyopathy have a different pathogenesis: the comprehensive physical examination to confirm that they pathogenesis of KSD mainly manifests as viral infection, had no heart disease. The clinical data of the KSD group cell membrane damage and oxidative stress (9). and control group are presented in Table 1. The present In recent years, the advances in RNA sequencing study was conducted in accordance with the Declaration of technology mean that it has developed into a powerful Helsinki (as revised in 2013) and was approved by the ethics research platform indispensable for exploring diseases. committee of Liaocheng People’s Hospital (No. 201510), At present, it is widely used for research into a variety of and all patients signed written informed consent. complex human diseases, such as malignant tumors, immune diseases and unknown infectious diseases, and it is crucial Main reagents and instruments to the search for pathogens and biomarkers, the exploration of pathogenesis, and the formulation of targeted treatment Main reagents: Trizol kit (Invitrogen life technologies, programs (10). In this study, RNA-sequence (RNA-seq, a USA), DEPC-treated water (Invitrogen life technologies, transcriptome sequencing technology) was used to construct USA), RNase inhibitor (Epicentre, USA), SuperScriptTM differential expression profiles of lncRNA in the peripheral III reverse transcriptase (Invitrogen, USA), 5× RT buffer blood plasma of KSD patients. These profiles were then (Invitrogen, USA), 2.5 mM dNTP mixture (HyTest © Cardiovascular Diagnosis and Therapy. All rights reserved. Cardiovasc Diagn Ther 2021;11(2):411-421 | http://dx.doi.org/10.21037/cdt-20-746 Cardiovascular Diagnosis and Therapy, Vol 11, No 2 April 2021 413 Ltd., Finland). Main instruments: NanoDrop ND-2000 to remove rRNAs from the RNA, and a TruSeq Stranded instrument (Thermo Fisher Scientific, USA), Ribo-Zero Total RNA Library Prep Kit (Illumina, USA) was used to rRNA Removal kits (Illumina, USA), TruSeq Stranded pre-process the RNA to construct a sequencing library. A Total RNA Library Prep Kit (Illumina, USA), BioAnalyzer BioAnalyzer 2100 instrument (Agilent Technologies, USA) 2100 instrument (Agilent Technologies, USA), Illumina was used for library quality control and quantification. In HiSeq4000 (Illumina, USA). accordance with the Illumina sequencing instructions, the 10 pM library was denatured into single-stranded DNA molecules, which were captured on an Illumina flow cell Experimental methods and amplified in situ into clusters. They then underwent Specimen acquisition 150 cycles of sequencing on the Illumina HiSeq sequencer. The subjects fasted for 12 hours, and blood was withdrawn from the elbow vein in the morning, after they had got up. Statistical analysis Five mL of peripheral venous blood was withdrawn from each subject in both the KSD group and the control group, Original data was obtained after sequencing by an Illumina with an anticoagulation negative pressure tube, and stored HiSeq4000 sequencer. The first quality control of the at −80 . raw data was performed using the Q30 value. Cutadapt software (v1.9.3) was used to remove adapters and low- ℃ RNA extraction quality reads, and then Hisat2 software (v2.0.4) was used The blood sample was removed from the −80 under the guidance of an Ensembl gtf gene annotation refrigerator, thawed, and centrifuged at 12,000 g at 4 for file to align high-quality adapter-free reads to the human ℃ 10 minutes to remove impurities.
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    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.